Locus 596

Sequence ID 2R_DroMel_CAF1
Location 3,034,749 – 3,034,885
Length 136
Max. P 0.864816
window1076 window1077 window1078 window1079

overview

Window 6

Location 3,034,749 – 3,034,869
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.61
Mean single sequence MFE -40.25
Consensus MFE -27.21
Energy contribution -27.05
Covariance contribution -0.16
Combinations/Pair 1.37
Mean z-score -2.08
Structure conservation index 0.68
SVM decision value 0.34
SVM RNA-class probability 0.695396
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3034749 120 + 20766785
GCAAUUGCCUGCAAGAAGAUCUGCUCCAUCCGCGAACAGUUCCUAAUGGCCUGCACCUUGGCACUGGCUAUCAUCUCGGCCAAUGCCUGCUGCACGUGCAGCAUUGUGACGCACUUGACC
.(((.(((..(((........)))......(((((.(((..((....)).)))......((((.(((((........))))).))))((((((....)))))))))))..))).)))... ( -35.80)
>DroVir_CAF1 7490 120 + 1
GCAACGGCUUGCAGAAAGAUCUGCUCCAGUCGUGAACAGUUCUUGAUAGCCUGCACCUUUGCACUGGCUAUCAUCUCGGCCAGCGCCUGCUGCACAUGCAGCAUAGUCACACACUUGGCU
((...((((.(((((....)))))...))))((((........((((((((((((....))))..))))))))....(((....)))((((((....))))))...)))).......)). ( -43.90)
>DroGri_CAF1 8409 120 + 1
GCAACGGCUUGCAGAAACAUCUGCUCCAGCCGCGAACAGUUCUUGAUGGCCUGCACUUUGGCGCUGGCAAUCAUUUCGGCCAGCGCUUGCUGCACAUGCAGCAUAUUCACGCACUUUACU
.....((((.(((((....)))))...))))(((..(((..(.....)..)))......(((((((((..........)))))))))((((((....))))))......)))........ ( -46.70)
>DroWil_CAF1 7903 116 + 1
GCCACUGCUUGGAGGAAAAUCUGCUCGAGUCGUGAACAAUUCUUGAUGGCCUGCACCUUGGCACUGGCUAUCAUCUCGGCCAGAGCCUGUUGGACAUGCAACAUUGUGACACAAUC----
..(((.((((((.((.....))..)))))).))).(((((..((((((.((.(((....(((.((((((........)))))).)))))).)).))).))).))))).........---- ( -34.40)
>DroMoj_CAF1 8841 120 + 1
GCAACGGCCUGCAGAAAAAUUUGCUCCAGACGCGAACAGUUUUUGAUGGCCUGCACCUUGGCACUGGCUAUCAUCUCGGCCAGCGCCUGCUGCACAUGCAGCAUCGUCACACACUUCAUU
(((..((((..((((((..(((((.......)))))...))))))..))))))).....(((.((((((........)))))).)))((((((....))))))................. ( -43.70)
>DroAna_CAF1 7961 120 + 1
GCCACCGCCUGUAGGAAGAUCUGCUCCAAGCGUGAACAGUUCUUAAUAGCUUGCACCUUGGCACUGGCAAUCAUUUCAGCCAGGGCCUGCUGUACAUGCAGCAUGGUCACGCACUUGACA
((((.....((((((((((.(((.(((....).)).))).)))).....))))))...)))).(((((..........)))))((((((((((....)))))).))))............ ( -37.00)
>consensus
GCAACGGCCUGCAGAAAGAUCUGCUCCAGCCGCGAACAGUUCUUGAUGGCCUGCACCUUGGCACUGGCUAUCAUCUCGGCCAGCGCCUGCUGCACAUGCAGCAUAGUCACACACUUGACU
((....))..(((((....))))).......(((.........(((((((((((......)))..))))))))....(((....)))((((((....))))))......)))........ (-27.21 = -27.05 +  -0.16) 

alignment

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secondary structure

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dotplot

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Window 7

Location 3,034,749 – 3,034,869
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.61
Mean single sequence MFE -43.50
Consensus MFE -34.63
Energy contribution -34.75
Covariance contribution 0.12
Combinations/Pair 1.33
Mean z-score -1.67
Structure conservation index 0.80
SVM decision value 0.37
SVM RNA-class probability 0.708350
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3034749 120 - 20766785
GGUCAAGUGCGUCACAAUGCUGCACGUGCAGCAGGCAUUGGCCGAGAUGAUAGCCAGUGCCAAGGUGCAGGCCAUUAGGAACUGUUCGCGGAUGGAGCAGAUCUUCUUGCAGGCAAUUGC
((((...(((..(....((((((....))))))(((((((((..........)))))))))..)..)))))))...((((.((((((.......)))))).))))...((((....)))) ( -47.00)
>DroVir_CAF1 7490 120 - 1
AGCCAAGUGUGUGACUAUGCUGCAUGUGCAGCAGGCGCUGGCCGAGAUGAUAGCCAGUGCAAAGGUGCAGGCUAUCAAGAACUGUUCACGACUGGAGCAGAUCUUUCUGCAAGCCGUUGC
.(((.(((.....))).((((((....)))))))))(((.((.((((((((((((.(..(....)..).)))))))).((.((((((.......)))))).)))))).)).)))...... ( -47.90)
>DroGri_CAF1 8409 120 - 1
AGUAAAGUGCGUGAAUAUGCUGCAUGUGCAGCAAGCGCUGGCCGAAAUGAUUGCCAGCGCCAAAGUGCAGGCCAUCAAGAACUGUUCGCGGCUGGAGCAGAUGUUUCUGCAAGCCGUUGC
........(((((((((((((((....)))))).((((((((..........))))))))......................)))))))((((...(((((....))))).))))...)) ( -47.00)
>DroWil_CAF1 7903 116 - 1
----GAUUGUGUCACAAUGUUGCAUGUCCAACAGGCUCUGGCCGAGAUGAUAGCCAGUGCCAAGGUGCAGGCCAUCAAGAAUUGUUCACGACUCGAGCAGAUUUUCCUCCAAGCAGUGGC
----......(((((..(((((......))))).(((.(((..((((((((.(((.(..(....)..).))).))))....((((((.......))))))..))))..)))))).))))) ( -34.40)
>DroMoj_CAF1 8841 120 - 1
AAUGAAGUGUGUGACGAUGCUGCAUGUGCAGCAGGCGCUGGCCGAGAUGAUAGCCAGUGCCAAGGUGCAGGCCAUCAAAAACUGUUCGCGUCUGGAGCAAAUUUUUCUGCAGGCCGUUGC
..........(..(((.((((((....))))))(((((((((..........)))))))))....((((((.....((((..(((((.......)))))..))))))))))...)))..) ( -42.80)
>DroAna_CAF1 7961 120 - 1
UGUCAAGUGCGUGACCAUGCUGCAUGUACAGCAGGCCCUGGCUGAAAUGAUUGCCAGUGCCAAGGUGCAAGCUAUUAAGAACUGUUCACGCUUGGAGCAGAUCUUCCUACAGGCGGUGGC
.((((..(((.(((((.(((((......)))))(((.(((((..........))))).)))..)))..........((((.((((((.......)))))).))))....)).))).)))) ( -41.90)
>consensus
AGUCAAGUGCGUGACAAUGCUGCAUGUGCAGCAGGCGCUGGCCGAGAUGAUAGCCAGUGCCAAGGUGCAGGCCAUCAAGAACUGUUCACGACUGGAGCAGAUCUUCCUGCAAGCCGUUGC
........((.......((((((....))))))(((((((((..........)))))))))....((((((.....((((.((((((.......)))))).)))))))))).))...... (-34.63 = -34.75 +   0.12) 

alignment

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secondary structure

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dotplot

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Window 8

Location 3,034,789 – 3,034,885
Length 96
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 82.44
Mean single sequence MFE -33.63
Consensus MFE -24.38
Energy contribution -24.63
Covariance contribution 0.25
Combinations/Pair 1.25
Mean z-score -2.32
Structure conservation index 0.72
SVM decision value 0.70
SVM RNA-class probability 0.825404
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3034789 96 + 20766785
UCCUAAUGGCCUGCACCUUGGCACUGGCUAUCAUCUCGGCCAAUGCCUGCUGCACGUGCAGCAUUGUGACGCACUUGACCGC---------------AGCCGUAUCAGCAA
.....(((((.(((.....((((.(((((........))))).))))((((((....)))))).................))---------------))))))........ ( -34.60)
>DroSec_CAF1 8424 96 + 1
UCCUAAUGGCCUGCACCUUGGCACUGGCUAUCAUCUCGGCCAAUGCCUGCUGCACGUGCAGCAUUGUGACGCACUUGACCGC---------------AGCCGUGUCAGCAA
.....(((((.(((.....((((.(((((........))))).))))((((((....)))))).................))---------------))))))........ ( -34.60)
>DroSim_CAF1 8433 96 + 1
UCCUGAUGGCCUGCACCUUGGCACUGGCUAUCAUCUCGGCCAAUGCCUGCUGCACGUGCAGCAUUGUGACGCACUUGACCGC---------------AGCCGUGUCAGCAA
..((((((((.(((.....((((.(((((........))))).))))((((((....)))))).................))---------------))))..)))))... ( -36.70)
>DroEre_CAF1 8874 96 + 1
UUCUAAUGGCCUGCACCUUGGCACUGGCUAUCAUCUCAGCCAAUGCCUGCUGUACGUGAAGCAUUGUUACGCACUUCACCGC---------------AGCCAUAUCAGCAA
.....(((((.(((.....((((.(((((........))))).))))........((((((...((.....)))))))).))---------------))))))........ ( -31.30)
>DroMoj_CAF1 8881 111 + 1
UUUUGAUGGCCUGCACCUUGGCACUGGCUAUCAUCUCGGCCAGCGCCUGCUGCACAUGCAGCAUCGUCACACACUUCAUUCCACCCGGCUGUGCGUCAGCUGUGUCAGCGA
...((((((..........(((.((((((........)))))).)))((((((....)))))))))))).............((.((((((.....)))))).))...... ( -38.80)
>DroPer_CAF1 11412 96 + 1
UCUUUAUGGCCUGUACCUUUGCGCUCGCUAUCAUCUCGCCAAGCGCCUGCUGCACGUGCAGCAUUGUCACACACUUAUCACG---------------AGCAGUGUCAGCUA
......((((((((......(((((.((.........))..))))).((((((....))))))...................---------------.)))).)))).... ( -25.80)
>consensus
UCCUAAUGGCCUGCACCUUGGCACUGGCUAUCAUCUCGGCCAAUGCCUGCUGCACGUGCAGCAUUGUGACGCACUUGACCGC_______________AGCCGUGUCAGCAA
.....(((((.........((((.(((((........))))).))))((((((....))))))...................................)))))........ (-24.38 = -24.63 +   0.25) 

alignment

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secondary structure

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dotplot

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Window 9

Location 3,034,789 – 3,034,885
Length 96
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 82.44
Mean single sequence MFE -38.57
Consensus MFE -29.50
Energy contribution -28.87
Covariance contribution -0.63
Combinations/Pair 1.32
Mean z-score -2.35
Structure conservation index 0.76
SVM decision value 0.84
SVM RNA-class probability 0.864816
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3034789 96 - 20766785
UUGCUGAUACGGCU---------------GCGGUCAAGUGCGUCACAAUGCUGCACGUGCAGCAGGCAUUGGCCGAGAUGAUAGCCAGUGCCAAGGUGCAGGCCAUUAGGA
..((((...)))).---------------..((((...(((..(....((((((....))))))(((((((((..........)))))))))..)..)))))))....... ( -39.10)
>DroSec_CAF1 8424 96 - 1
UUGCUGACACGGCU---------------GCGGUCAAGUGCGUCACAAUGCUGCACGUGCAGCAGGCAUUGGCCGAGAUGAUAGCCAGUGCCAAGGUGCAGGCCAUUAGGA
..((((...)))).---------------..((((...(((..(....((((((....))))))(((((((((..........)))))))))..)..)))))))....... ( -39.10)
>DroSim_CAF1 8433 96 - 1
UUGCUGACACGGCU---------------GCGGUCAAGUGCGUCACAAUGCUGCACGUGCAGCAGGCAUUGGCCGAGAUGAUAGCCAGUGCCAAGGUGCAGGCCAUCAGGA
...((((...((((---------------((......))((..(....((((((....))))))(((((((((..........)))))))))..)..)).)))).)))).. ( -39.80)
>DroEre_CAF1 8874 96 - 1
UUGCUGAUAUGGCU---------------GCGGUGAAGUGCGUAACAAUGCUUCACGUACAGCAGGCAUUGGCUGAGAUGAUAGCCAGUGCCAAGGUGCAGGCCAUUAGAA
...((((..(((((---------------...(((((((..........)))))))((((....(((((((((((......)))))))))))...)))).))))))))).. ( -40.00)
>DroMoj_CAF1 8881 111 - 1
UCGCUGACACAGCUGACGCACAGCCGGGUGGAAUGAAGUGUGUGACGAUGCUGCAUGUGCAGCAGGCGCUGGCCGAGAUGAUAGCCAGUGCCAAGGUGCAGGCCAUCAAAA
.......(((.((((.....))))...)))...(((.((.(((..(..((((((....))))))(((((((((..........)))))))))..)..))).))..)))... ( -42.00)
>DroPer_CAF1 11412 96 - 1
UAGCUGACACUGCU---------------CGUGAUAAGUGUGUGACAAUGCUGCACGUGCAGCAGGCGCUUGGCGAGAUGAUAGCGAGCGCAAAGGUACAGGCCAUAAAGA
...(((...((((.---------------((((...(((((......))))).)))).)))))))(((((((.(.........))))))))...(((....)))....... ( -31.40)
>consensus
UUGCUGACACGGCU_______________GCGGUCAAGUGCGUCACAAUGCUGCACGUGCAGCAGGCAUUGGCCGAGAUGAUAGCCAGUGCCAAGGUGCAGGCCAUUAGGA
..((((.((((((................((......))((((....)))).)).)))))))).(((((((((..........)))))))))..(((....)))....... (-29.50 = -28.87 +  -0.63) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:26 2006